Assignment

I've upgraded to Moodle 1.7, and using DownThemAll 0.9.9.7, and FireFox 2.0. When students submit assignments to me, if the assignments are .txt or .java files, the contents of the files are being converted to html, and when I download them, a .html extension is being added. Is there a setting I have missed? I did not have this problem before the upgrade. I wouldn't mind too much having to rename the files to remove the .html extension, but html tags are actually being placed inside the files. Any help would be appreciated. This is not happening with .doc, .ppt, .rtf files, just the plain text files (.txt and .java)
The .html extension is not showing up when I look at the submission page, so I'm thinking the tags are being added on upload, but am not sure.

Thanks in advance,